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software:topical:lifescience [2019/03/12 08:31]
meesters [Annotation Tools]
software:topical:lifescience [2020/02/11 19:13] (current)
meesters [Various -- Software Collections]
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 You can ask for updates on a particular software or to install previously not supported software [[https://​hpc.uni-mainz.de/​high-performance-computing/​service-angebot/​softwareinstallation/​|via our webpage]]. You can ask for updates on a particular software or to install previously not supported software [[https://​hpc.uni-mainz.de/​high-performance-computing/​service-angebot/​softwareinstallation/​|via our webpage]].
 +
 +<WRAP center round info 90%>
 +If an installed tool is not listed on this page, respectively its underlying links, you may contribute this (its a wiki!) or ask for further documentation.
 +</​WRAP>​
 +
 +===== R and Bioconductor =====
 +
 +The information on R and Bioconductor merits a [[software:​topical:​lifescience:​R_Bioconductor|separate page]].
  
 ===== NGS & Co. ===== ===== NGS & Co. =====
  
  
-==== NGS Preprocessing Software ====+==== NGS Preprocessing Software ​and other Quality Checks ​====
  
   * [[software:​topical:​lifescience:​QA|Quality Assessment Tools]]   * [[software:​topical:​lifescience:​QA|Quality Assessment Tools]]
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 ==== Mapping Tools ==== ==== Mapping Tools ====
  
-  * [[software:​topical:​lifescience:​ngs_read_mapping_tools|NGS Read-Mapping Tools: BWA, Bowtie and STAR]]+  * [[software:​topical:​lifescience:​ngs_read_mapping_tools|NGS Read-Mapping Tools]]
  
 +==== Variant Calling Tools ====
 +
 +  * [[software:​topical:​lifescience:​variant_calling_tools|Variant Calling Tools]]
 ==== Intermediate Processing ==== ==== Intermediate Processing ====
  
   * [[software:​topical:​lifescience:​sdi|Sorting,​ Deduplication and Indexing of BAM files]]   * [[software:​topical:​lifescience:​sdi|Sorting,​ Deduplication and Indexing of BAM files]]
 +
 +==== *-Seq Analysis ====
 +
 +  * [[software:​topical:​lifescience:​transcript_abundance_tools|Assessing Transcript Abundance]]
  
 ==== Annotation Tools / Local Search Tools ==== ==== Annotation Tools / Local Search Tools ====
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 ==== Various -- Software Collections ==== ==== Various -- Software Collections ====
  
-  * [[software:​topical:​lifescience:​seqan|SeqAn]] -- efficient applications of different areas * +  * [[software:​topical:​lifescience:​seqan|SeqAn]] -- efficient applications of different areas  
-  * [[software:​topical:​lifescience:​bbmap|BBMap]] -- short read aligner + other tools *+  * [[software:​topical:​lifescience:​bbmap|BBMap]] -- short read aligner + other tools  
 +  ​[[software:​topical:​lifescience:​sra|SRA toolkit]] -- the NCBI SRA toolkit on mogon
  
-===== Genome Assembly ===== 
- 
-  * [[software:​topical:​lifescience:​trinity|Trinity]] * 
  
 ===== Evolutionary & Phylogenetics Software Tools ===== ===== Evolutionary & Phylogenetics Software Tools =====
  
 +  * [[software:​topical:​lifescience:​genome_assembly|Genome Assembly Tools]]
 +  * [[software:​topical:​lifescience:​phylogenic_reconstruction|Phylogenetic Reconstruction]]
 +  * [[software:​topical:​lifescience:​multiple_sequence_alignment|Multiple Sequence Alignment]]
 +  * [[software:​topical:​lifescience:​population_genetics|General Population Genetics]]
  
-  * [[software:​topical:​lifescience:​ipyrad|IPyrad]] 
  
 ===== Molecular Docking Tools ===== ===== Molecular Docking Tools =====
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   * [[software:​topical:​physics:​vmd_namd|Using VMD and NAMD on Mogon]]   * [[software:​topical:​physics:​vmd_namd|Using VMD and NAMD on Mogon]]
  
 +===== Single Particle Processing / Analysis =====
 +
 +  * [[software:​topical:​lifescience:​cistem|Using cisTEM]]
 +  * [[software:​topical:​lifescience:​relion|Using RELION]]
 +
 +===== Development =====
 +
 +  * [[software:​topical:​lifescience:​seqan3|The SeqAn C++ library for sequence analysis]]
  
 ===== What Else? ===== ===== What Else? =====
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     * we install software in an optimized fashion     * we install software in an optimized fashion
     * if installed as a module, we made the commitment to support the software, if there are issues with the module, the batch system or I/O((but, of course, not with respect to bugs within the software))     * if installed as a module, we made the commitment to support the software, if there are issues with the module, the batch system or I/O((but, of course, not with respect to bugs within the software))
-  - Writing wrapper scripts for otherwise non-performant applications can be cumbersome. We still encourage to approach us and ask us, before being stuck in a project.+  - Writing wrapper scripts for otherwise non-performant applications can take time. We still encourage to approach us and ask us, before being stuck in a project.
  
 +<WRAP center round info 90%>
 Any contribution (a script, an idea, a reported issue, feature request, documentation,​ test data, own benchmark, etc.) is welcome! Particularly,​ section links labeled with "​*"​ require attention((Missing links wait to be filled with content - a re-structuring might also occur.)). Any contribution (a script, an idea, a reported issue, feature request, documentation,​ test data, own benchmark, etc.) is welcome! Particularly,​ section links labeled with "​*"​ require attention((Missing links wait to be filled with content - a re-structuring might also occur.)).
 +
 +  * [[https://​mogonwiki.zdv.uni-mainz.de/​dokuwiki/​training_and_outreach:​faq#​may_i_contribute_to_this_wiki|Here is info on how to contribute to documentation]].
 +  * If you have written a piece of software (e.g. a script for a particular workflow) you would like to share, please [[hpc@uni-mainz.de|do not hesitate to approach us]].
 +</​WRAP>​
 +
 +<WRAP center round info 90%>
 +**Tired of //​[[https://​en.wikipedia.org/​wiki/​Software_as_a_service|Software as a Service]]//?​**
 +
 +  * You have the option to collaborate on specific setups or if a specific tool needs to be written.
 +  * Any feedback will help.
 +</​WRAP>​
            
software/topical/lifescience.1552375891.txt.gz · Last modified: 2019/03/12 08:31 by meesters